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Selecting and Exporting Multiple Regions of Interest

Selecting and Exporting Multiple Regions of Interest

The Selections pop-up window allows you to view and export information about selected regions. Selections lists both selected Regions of Interest (ROIs) and selected cells in the drop-down menu of the pop-up window.

The lasso tool allows you to create multiple ROI selections with both the rectangle and freehand lassos. You can also make overlapping selections.

To select specific cells, make sure tooltips are turned on (Settings > Show Tooltips). View cells (outlined or filled) and click on the cell of interest. It will be added to the list of Selections. If you click on a cell that is completely within an active ROI selection, the selection box will show cell statistics for the cell within the selection instead of adding a new cell ID to the list of Selections. To add the cell as its own cell selection, switch to a different active selection or close the Selections window.

The following information is displayed for each selection.

TabsSelected ROISelected cell
InfoArea, total transcript count*, total cell countCluster assignment from clustering type selected in Cells menu, transcript count*, cell area, X-Y location, segmentation description
TranscriptsCount and density per transcript in the selection for genes checked in the Transcripts menuCount and density per transcript in the cell for genes checked in the Transcripts menu
CellsFor cells completely contained in the selection: cell count and area per cluster for clustering type selected in Cells menu, cluster assignment, transcript count, cell area per cell, cell ID from the All Cells tab (with links to cell-specific statistics)(Not applicable)

*Transcript counts in selected ROIs are derived from transcript assignments by cell segmentation polygon boundaries, which are used in Xenium Explorer as approximations for visualization performance. Transcript counts in selected cells are derived from transcript assignments by cell segmentation masks in the cell-feature matrix.

There is an updated format for cell IDs in output files generated by Xenium Onboard Analysis (XOA) v1.3 and later. Xenium Explorer v1.1 and later will display pre-v1.3 XOA data with the original integer format and v1.3+ XOA data with the new format. Please upgrade to the latest version of Xenium Explorer to view data from Xenium Onboard Analysis v1.3+ (also see [release notes])(/support/software/xenium-explorer/latest/release-notes/release-notes-for-XE).

Selected ROIs and cells are automatically labeled, but both can be renamed.


Add another selection

Use the Add another selection icon on the Selections pop-up window to draw a new selection.


You can also click on the lasso tool to draw a new selection and it will be added to the Selections pop-up window

Selected ROIs and cells are collected into the same Selections window. The drop-down menu allows you to switch between selected ROIs and cells. The Go to selection icon allows you to jump to a specific selection in the viewing area.


You can export selection coordinates, transcript stats, and cell and cluster stats from the Selections window.

The download icon at the top of the Selections window allows you to export coordinates for all selected ROIs and cells to a CSV file.


Here’s an example - the header lists the selected ROI and cell ID names:

#Selection names:,"Cell amcmlpgl-1, Cell cmlbdfdf-1, Selection 1"
"#Areas (µm^2): 688.59, 351.50, 613841.19"
Selection,X,Y
Cell amcmlpgl-1,4211.42,4894.09
Cell amcmlpgl-1,4202.54,4896.13
[ … ]
Cell cmlbdfdf-1,4204.03,4954.23
Cell cmlbdfdf-1,4199.78,4954.84
[ … ]
Selection 1,6261.68,3939.25
Selection 1,6305.02,3906.91
[ … ]

You can also export coordinates for a specific selection. Click the three dots next to the drop-down menu and either Copy Selection Coordinates or Download Selection Coordinates as CSV.


Example:

#Selection name: Selection 1
#Area (µm^2): 613841.19
X,Y
6261.68,3939.25
6305.02,3906.91
6331.58,3903.46
6412.56,3906.17
6479.70,3911.10
[ ... ]

Click the three vertical dots on the Transcripts tab to copy or download a CSV file of transcript stat information.


Example:

#Selection name: Selection 1
#Area (µm^2): 613841.19
#Panel genes not included:
Gene,Count,Density (µm^-2)
ABCC11,6060,0.00987226032762517
ACTA2,5773,0.009404712685046222
ACTG2,7587,0.012359874439883196
ADAM9,6105,0.00994556919144417
ADGRE5,531,0.0008650445930641857
ADH1B,191,0.00031115539976508375
[ ... ]

Click the three vertical dots on the Cells tab to copy or download a CSV file of cell stats or cluster stats information.

Starting in Xenium Explorer v1.2, cell IDs can be exported for ROI selections ("Download Cell Stats as CSV").


Example of cluster stats:

#Selection name: Selection 1
#Area (µm^2): 613841.19
"#Clusters not included: "
Cluster,Count,Area (µm^2)
Cluster 1,21,2502.94
Cluster 2,73,10251.44
[...]

Example of cell stats (cell ID format depends on Xenium Onboard Analysis pipeline version):

#Selection name: Selection 1
#Area (µm^2): 70724.26
Cell ID,Cluster,Transcripts,Area (µm^2)
aamcdkdi-1,Cluster 5,200,145.35
aaiegbme-1,Cluster 12,90,59.89
aajmbhof-1,Cluster 12,45,30.67
bmfkhcap-1,Cluster 5,21,16.53
bmefpfba-1,Cluster 5,19,13.72
bmdnodcp-1,Cluster 5,80,60.33
[...]

Selections can be saved with the Save Current View function. Learn more in the Saving and Sharing Results tutorial.

You can also copy the selection lasso shape or cell coordinates from the Selections window and paste with the Lasso > Paste coordinates button. The copied coordinates will not be displayed on the screen, but the Selections window will then re-display information for the selected region.


To test, you can open a new Xenium Explorer window (File > New Window) and paste the selection coordinates. The first selection in this new window now displays the same ROI information that was created above (including Transcripts and Cells tab information for whichever genes and/or cell clusters are checked in their respective menus).


To delete all selections, click the trash can icon at the top of the Selections window.


There are two ways to delete specific selections:

  1. Click the three dots next to the drop-down menu and click Remove Selection.

  1. Click the trash can icon in the drop-down menu.